WO2006113678A3 - Methylation markers for diagnosis and treatment of cancers - Google Patents

Methylation markers for diagnosis and treatment of cancers Download PDF

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Publication number
WO2006113678A3
WO2006113678A3 PCT/US2006/014500 US2006014500W WO2006113678A3 WO 2006113678 A3 WO2006113678 A3 WO 2006113678A3 US 2006014500 W US2006014500 W US 2006014500W WO 2006113678 A3 WO2006113678 A3 WO 2006113678A3
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WO
WIPO (PCT)
Prior art keywords
silenced
restoration
markers
accomplished
treatments
Prior art date
Application number
PCT/US2006/014500
Other languages
French (fr)
Other versions
WO2006113678A2 (en
Inventor
Criekinge Wim Van
Josef Straub
Bea Wisman
Original Assignee
Oncomethylome Sciences Inc
Criekinge Wim Van
Josef Straub
Bea Wisman
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Oncomethylome Sciences Inc, Criekinge Wim Van, Josef Straub, Bea Wisman filed Critical Oncomethylome Sciences Inc
Priority to CA002604689A priority Critical patent/CA2604689A1/en
Priority to EP06758387A priority patent/EP1869224A4/en
Priority to US11/887,616 priority patent/US20090203639A1/en
Publication of WO2006113678A2 publication Critical patent/WO2006113678A2/en
Publication of WO2006113678A3 publication Critical patent/WO2006113678A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/04—Antineoplastic agents specific for metastasis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

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  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Pathology (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Oncology (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biophysics (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Animal Behavior & Ethology (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

Two hundred ten markers are provided which are epigenetically silenced in one or more cancer types. The markers can be used diagnostically, prognostically, therapeutically, and for selecting treatments that are well tailored for an individual patient. Restoration of expression of silenced genes can be useful therapeutically, for example, if the silenced gene is a tumor-suppressor gene. Restoration can be accomplished by supplying non-methylated copies of the silenced genes or polynucleotides encoding their encoded products. Alternatively, restoration can be accomplished using chemical demethylating agents or methylation inhibitors. Kits for testing for epigenetic silencing can be used in the context of diagnostics, prognostics, or for selecting 'personalized medicine' treatments.
PCT/US2006/014500 2005-04-15 2006-04-17 Methylation markers for diagnosis and treatment of cancers WO2006113678A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
CA002604689A CA2604689A1 (en) 2005-04-15 2006-04-17 Methylation markers for diagnosis and treatment of cancers
EP06758387A EP1869224A4 (en) 2005-04-15 2006-04-17 Methylation markers for diagnosis and treatment of cancers
US11/887,616 US20090203639A1 (en) 2005-04-15 2006-04-17 Methylation Markers for Diagnoses and Treatment of Cancers

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US67150105P 2005-04-15 2005-04-15
US60/671,501 2005-04-15

Publications (2)

Publication Number Publication Date
WO2006113678A2 WO2006113678A2 (en) 2006-10-26
WO2006113678A3 true WO2006113678A3 (en) 2009-06-18

Family

ID=37115840

Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2006/014493 WO2006113671A2 (en) 2005-04-15 2006-04-17 Methylation markers for diagnosis and treatment of cancers
PCT/US2006/014500 WO2006113678A2 (en) 2005-04-15 2006-04-17 Methylation markers for diagnosis and treatment of cancers

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/US2006/014493 WO2006113671A2 (en) 2005-04-15 2006-04-17 Methylation markers for diagnosis and treatment of cancers

Country Status (4)

Country Link
US (3) US20100035970A1 (en)
EP (2) EP1869222A4 (en)
CA (2) CA2604852A1 (en)
WO (2) WO2006113671A2 (en)

Families Citing this family (37)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090269736A1 (en) * 2002-10-01 2009-10-29 Epigenomics Ag Prognostic markers for prediction of treatment response and/or survival of breast cell proliferative disorder patients
DE602004031405D1 (en) * 2003-12-11 2011-03-31 Epigenomics Ag Marker to predict the response to therapy or the survival rate of breast cancer patients
SI1642905T1 (en) 2004-10-02 2009-04-30 Immatics Biotechnologies Gmbh Immunogenic T-helper epitopes from human tumour antigens and immunotherapeutic methods using said epitopes
EP1907855A4 (en) * 2005-07-12 2009-11-11 Univ Temple Genetic and epigenetic alterations in the diagnosis and treatment of cancer
WO2007030930A1 (en) 2005-09-13 2007-03-22 National Research Council Of Canada Methods and compositions for modulating tumor cell activity
US7754428B2 (en) * 2006-05-03 2010-07-13 The Chinese University Of Hong Kong Fetal methylation markers
ES2539042T3 (en) * 2006-06-02 2015-06-25 Glaxosmithkline Biologicals S.A. Identification procedure of whether a patient will respond to immunotherapy or not
US7888127B2 (en) 2008-01-15 2011-02-15 Sequenom, Inc. Methods for reducing adduct formation for mass spectrometry analysis
CA2715774A1 (en) * 2008-02-19 2009-08-27 Oncomethylome Sciences Sa Detection and prognosis of lung cancer
US20110189653A1 (en) 2008-03-21 2011-08-04 Wim Van Criekinge Detection and prognosis of cervical cancer
US8372587B2 (en) * 2008-04-14 2013-02-12 Nihon University Proliferative disease detection method
BRPI0913578A2 (en) 2008-05-14 2017-06-06 Dermtech Int diagnosis of melanoma and solar lentigo by nucleic acid analysis
EP2297336A1 (en) * 2008-05-29 2011-03-23 Vib Vzw Minichromosome maintenance complex interacting protein involved in cancer
US9023819B2 (en) 2008-06-09 2015-05-05 National Chung Cheng University Treatment of a disease or a condition associated with aberrant gene hypomethylation by a method involving tailored epigenomic modification
US8053189B2 (en) * 2008-11-03 2011-11-08 Fina Biotech, S.L.U. Method for the diagnosis of colorectal cancer
EP2233590A1 (en) * 2009-01-28 2010-09-29 AIT Austrian Institute of Technology GmbH Methylation assay
US20120164238A1 (en) 2009-02-03 2012-06-28 Mdxhealth Sa Methods of detecting colorectal cancer
US8715928B2 (en) * 2009-02-13 2014-05-06 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Molecular-based method of cancer diagnosis and prognosis
EP2428584A4 (en) * 2009-04-03 2012-10-10 A & T Corp Method for detection of colorectal tumor
WO2011004837A1 (en) 2009-07-08 2011-01-13 株式会社ＡＣＴＧｅｎ Antibody having anti-cancer activity
WO2011036173A1 (en) * 2009-09-24 2011-03-31 Oncomethylome Sciences S.A. Detection and prognosis of cervical cancer
CA2928846A1 (en) 2009-11-24 2011-06-03 Alethia Biotherapeutics Inc. Anti-clusterin antibodies and antigen binding fragments and their use to reduce tumor volume
EP2598659B1 (en) 2010-07-27 2015-03-11 Genomic Health, Inc. Method for using gene expression to determine prognosis of prostate cancer
US20120202202A1 (en) * 2011-01-28 2012-08-09 Michael Xia Wang Methods for detecting rare circulating cancer cells using dna methylation biomarkers
US20140031257A1 (en) * 2011-03-10 2014-01-30 Oslo Universitetssykehus Hf Methods and biomarkers for detection of gastrointestinal cancers
ES2675727T3 (en) 2012-02-13 2018-07-12 Beijing Institute For Cancer Research Method for in vitro estimation of tumorigenesis, metastasis or life expectancy and artificial nucleotide used
CN104159611A (en) 2012-02-22 2014-11-19 阿莱斯亚生物疗法股份有限公司 Co-use of a clusterin inhibitor with an EGFR inhibitor to treat cancer
US20130189684A1 (en) * 2013-03-12 2013-07-25 Sequenom, Inc. Quantification of cell-specific nucleic acid markers
US9305756B2 (en) 2013-03-13 2016-04-05 Agena Bioscience, Inc. Preparation enhancements and methods of use for MALDI mass spectrometry
EP2806274A1 (en) * 2013-05-24 2014-11-26 AIT Austrian Institute of Technology GmbH Lung cancer diagnostic method and means
WO2016116922A1 (en) * 2015-01-19 2016-07-28 Rappaport Family Institute For Research In The Medical Sciences Ubiquitin ligase kpc1 promotes processing of p105 nf-kappab1 to p50, eliciting strong tumor suppression
WO2018127786A1 (en) * 2017-01-06 2018-07-12 Oslo Universitetssykehus Hf Compositions and methods for determining a treatment course of action
AU2018251770B2 (en) * 2017-04-10 2024-03-14 Dermtech, Inc. Non-invasive skin-based detection methods
US11242568B2 (en) * 2017-12-29 2022-02-08 City Of Hope DNA methylation diagnostic test for breast cancer
CA3090785A1 (en) 2018-02-14 2019-08-22 John Daniel Dobak Iii Novel gene classifiers and uses thereof in non-melanoma skin cancers
US11578373B2 (en) 2019-03-26 2023-02-14 Dermtech, Inc. Gene classifiers and uses thereof in skin cancers
CN110885375B (en) * 2019-12-20 2021-07-02 南京融捷康生物科技有限公司 Single-domain antibody specifically aiming at MMP-9 protein zinc ion binding domain, product and application

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2004083399A2 (en) * 2003-03-17 2004-09-30 The Johns Hopkins University Aberrantly methylated genes in pancreatic cancer

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5783672A (en) * 1994-05-26 1998-07-21 Immunex Corporation Receptor for oncostatin M
WO2002057414A2 (en) * 2000-10-20 2002-07-25 Expression Diagnostics, Inc. Leukocyte expression profiling
AU2002351828A1 (en) * 2001-11-05 2003-05-19 Deutsches Krebsforschungszentrum Novel genetic markers for leukemias
WO2003042661A2 (en) * 2001-11-13 2003-05-22 Protein Design Labs, Inc. Methods of diagnosis of cancer, compositions and methods of screening for modulators of cancer
EP2230299B1 (en) * 2002-01-18 2011-12-07 ZymoGenetics, Inc. Novel cytokine ZCYTOR17 ligand
IL163732A0 (en) * 2002-03-07 2005-12-18 Univ Johns Hopkins Genomic screen for epigenetically silenced tumor suppressor genes
US20040053304A1 (en) * 2002-06-05 2004-03-18 Case Western Reserve University Methods and compositions for detecting cancers
WO2004087957A2 (en) * 2003-04-03 2004-10-14 Oncomethylome Sciences S.A. Hypermethylated genes and cervical cancer
EP2003196A3 (en) * 2003-06-09 2009-01-07 The Regents of the University of Michigan Compositions and methods for treating and diagnosing cancer

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2004083399A2 (en) * 2003-03-17 2004-09-30 The Johns Hopkins University Aberrantly methylated genes in pancreatic cancer

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
KITKUMTHORN ET AL.: "Cyclin A1 promoter hypermethylation in human papillomavirus- associated cervical cancer.", BMC CANCER., vol. 6, no. 55, 8 March 2006 (2006-03-08), pages 1 - 9, XP008123611 *
MULLER ET AL.: "Methylation of the cyclin A1 promoter correlates with gene silencing in somatic cell lines, while tissue-specific expression of cyclin A1 is methylation independent.", MOLECULAR AND CELLULAR BIOLOGY., vol. 20, no. 9, May 2000 (2000-05-01), pages 3316 - 3329, XP002978075 *
See also references of EP1869224A4 *
TOKUMARU ET AL.: "Inverse correlation between cyclin A1 hypermethylation and p53 mutation in head and neck cancer identified by reversal of epigenetic silencing.", CANCER RESEARCH., vol. 64, 1 September 2004 (2004-09-01), pages 5982 - 5987, XP008123553 *

Also Published As

Publication number Publication date
EP1869224A4 (en) 2009-11-18
EP1869222A4 (en) 2010-01-20
US20090203639A1 (en) 2009-08-13
WO2006113671A3 (en) 2009-04-23
WO2006113678A2 (en) 2006-10-26
CA2604689A1 (en) 2006-10-26
CA2604852A1 (en) 2006-10-26
US20100035970A1 (en) 2010-02-11
WO2006113671A2 (en) 2006-10-26
WO2006113671A8 (en) 2007-06-07
EP1869224A2 (en) 2007-12-26
EP1869222A2 (en) 2007-12-26
US20090215709A1 (en) 2009-08-27

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